4GLI | pdb_00004gli

Crystal Structure of Human SMN YG-Dimer

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d4glia_	Alpha and beta proteins (a/b)	Periplasmic binding protein-like II	Periplasmic binding protein-like II	automated matches	automated matches	bacteria, human (Escherichia coli ) [TaxId: 562 ], bacteria, human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Type 2 solute binding protein-like	8058187	3000083	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A		e4gliA1	A: Alpha-beta plaits	X: Adenylyl and guanylyl cyclase catalytic domain-like	H: Adenylyl and guanylyl cyclase catalytic domain-like	T: SBP_bac_1	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01547	Bacterial extracellular solute-binding protein (SBP_bac_1)	Bacterial extracellular solute-binding protein	-	Family
A	PF20635	Survival Motor Neuron, YG-box (SMN_YG-box)	Survival Motor Neuron, YG-box	Survival Motor Neuron (SMN) protein forms the oligomeric core of a multi-protein complex that functions in spliceosomal snRNP biogenesis. Mutations in the SMN gene cause spinal muscular atrophy (SMA). It has three highly conserved domains: a short N- ...	Survival Motor Neuron (SMN) protein forms the oligomeric core of a multi-protein complex that functions in spliceosomal snRNP biogenesis. Mutations in the SMN gene cause spinal muscular atrophy (SMA). It has three highly conserved domains: a short N-terminal segment responsible for binding with high affinity to Gemin2, therefore, called Gemin2-binding domain (G2-BD), a central Tudor domain (Pfam:PF06003) that recognises symmetric dimethylarginine (sDMA) modifications in proteins involved in RNA processing, and a C-terminal domain, represented in this entry, referred to as the 'YG-box' [1,2]. This domain contains three overlapping motifs: GxxxGxxxG, YxxxYxxxY and SxxxSxxxSxxxT. The YG-box forms helical oligomers similar to the glycine zippers found in transmembrane channels. The YG-box oligomers are thought to be involved in oligomerization and are likely to be used directly in mediating interactions that are crucial for SMN's functions [1]. It has been reported that nearly half of the known SMA patient missense mutations map to the SMN YG-box [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Maltose-binding periplasmic protein, Survival motor neuron protein chimera	transporter activity carbohydrate transmembrane transporter activity transmembrane transporter activity oligosaccharide binding binding disaccharide binding carbohydrate binding maltose binding RNA binding nucleic acid binding identical protein binding protein binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process cell chemotaxis chemotaxis response to external stimulus cellular response to chemical stimulus taxis response to chemical cell migration cell motility cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process cell chemotaxis chemotaxis response to external stimulus cellular response to chemical stimulus taxis response to chemical cell migration cell motility locomotion localization transport carbohydrate transport oligosaccharide transport disaccharide transport establishment of localization maltose transport polysaccharide localization dextrin transport macromolecule localization maltodextrin transmembrane transport polysaccharide transport response to disaccharide response to oxygen-containing compound detection of maltose stimulus detection of stimulus response to carbohydrate detection of chemical stimulus detection of disaccharide stimulus response to maltose detection of carbohydrate stimulus RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression DNA-templated transcription termination macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process macromolecule metabolic process ribonucleoprotein complex biogenesis mRNA processing protein-RNA complex assembly cellular component organization cellular component biogenesis protein-RNA complex organization cellular component assembly protein-containing complex assembly cellular component organization or biogenesis RNA processing RNA splicing protein-containing complex organization spliceosomal snRNP assembly mRNA metabolic process RNA splicing, via transesterification reactions mRNA splicing, via spliceosome RNA splicing, via transesterification reactions with bulged adenosine as nucleophile spliceosomal complex assembly developmental process multicellular organism development multicellular organismal process anatomical structure development nervous system development system development	ATPase dependent transmembrane transport complex protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex transporter complex ATP-binding cassette (ABC) transporter complex cell periphery cellular anatomical structure transmembrane transporter complex ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing maltose transport complex periplasmic space ATPase dependent transmembrane transport complex protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex transporter complex ATP-binding cassette (ABC) transporter complex cell periphery cellular anatomical structure transmembrane transporter complex ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing maltose transport complex periplasmic space outer membrane-bounded periplasmic space cell envelope somatodendritic compartment cell body perikaryon neuronal cell body intracellular anatomical structure intracellular membraneless organelle Z disc sarcomere intracellular organelle I band organelle membraneless organelle contractile muscle fiber cytoplasm supramolecular fiber myofibril supramolecular polymer supramolecular complex cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nuclear body nucleoplasm organelle lumen nuclear lumen Gemini of Cajal bodies cell projection neuron projection plasma membrane bounded cell projection SMN-Sm protein complex Sm-like protein family complex cytoplasmic ribonucleoprotein granule ribonucleoprotein granule Cajal body nuclear ribonucleoprotein granule SMN complex axon

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR006061	Solute-binding family 1, conserved site	Conserved Site
A	IPR006060	Maltose/Cyclodextrin ABC transporter, substrate-binding protein	Family
A	IPR006059	Bacterial-type extracellular solute-binding protein	Family
A	IPR002999	Tudor domain	Domain
A	IPR047313	Survival motor neuron protein, C-terminal oligomerization domain	Domain
A	IPR049481	Survival Motor Neuron, Gemin2-binding domain	Domain
A	IPR010304	Survival motor neuron, Tudor domain	Domain
A	IPR047298	Survival motor neuron protein, Tudor domain, eumetazoa	Domain
A	IPR040424	SMN complex subunit Smn1	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q16637	spinal muscular atrophy, type III spinal muscular atrophy amyotrophic lateral sclerosis Spinal muscular atrophy 4 spinal muscular atrophy, type 1 spinal muscular atrophy, type IV neurodegenerative disease progressive muscular atrophy spinal muscular atrophy, type II muscular atrophy peripheral neuropathy Charcot-Marie-Tooth disease

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.